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NM_020822.3(KCNT1):c.299G>A (p.Arg100Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Apr 12, 2019)
Last evaluated:
Mar 14, 2017
Accession:
VCV000196502.2
Variation ID:
196502
Description:
single nucleotide variant
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NM_020822.3(KCNT1):c.299G>A (p.Arg100Gln)

Allele ID
193663
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.3
Genomic location
9: 135750142 (GRCh38) GRCh38 UCSC
9: 138641988 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.138641988G>A
NC_000009.12:g.135750142G>A
NM_020822.3:c.299G>A MANE Select NP_065873.2:p.Arg100Gln missense
... more HGVS
Protein change
R100Q, R52Q
Other names
-
Canonical SPDI
NC_000009.12:135750141:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00003
Links
ClinGen: CA243474
dbSNP: rs752032951
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 14, 2017 RCV000177321.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNT1 - - GRCh38
GRCh37
1216 1274

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 23, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000229168.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Mar 14, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000983824.1
Submitted: (Apr 12, 2019)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KCNT1 - - - -

Text-mined citations for rs752032951...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Feb 27, 2021